ArticleScientific reports2018
Intensify3D: Normalizing signal intensity in large heterogenic image stacks.
Article in Scientific reports, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 21 papers.
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Who cites it
21 citing papers in PubMed, 32 citations in OpenAlex.
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- Pleomorphism in Biological Units of Life: Morphological Heterogeneity in Cells Does Not Translate Uniformly to Subcellular Components.ACS omega · 2024Article
- ProDiVis: a method to normalize fluorescence signal localization in 3D specimens.Frontiers in cell and developmental biology · 2024Article
- Accounting for intensity variation in image analysis of large-scale multiplexed clinical trial datasets.The journal of pathology. Clinical research · 2023Article
- Imaging and quantification of the tumor microenvironment of triple negative breast cancer using TPEF and scanning laser optical tomography.Biomedical optics express · 2023Article
- High-throughput morphometric and transcriptomic profiling uncovers composition of naïve and sensory-deprived cortical cholinergic VIP/CHAT neurons.The EMBO journal · 2023Article
- Segmentation of Tissues and Proliferating Cells in Light-Sheet Microscopy Images of Mouse Embryos Using Convolutional Neural Networks.IEEE access : practical innovations, open solutions · 2022Article
- It's clearly the heart! Optical transparency, cardiac tissue imaging, and computer modelling.Progress in biophysics and molecular biology · 2022Article
- Expansion Microscopy of Larval Zebrafish Brains and Zebrafish Embryos.Methods in molecular biology (Clifton, N.J.) · 2022Article
- Single Image-Based Vignetting Correction for Improving the Consistency of Neural Activity Analysis in 2-Photon Functional Microscopy.Frontiers in neuroinformatics · 2021Article
- Young adult-born neurons improve odor coding by mitral cells.Nature communications · 2020Article
- Barrel cortex VIP/ChAT interneurons suppress sensory responses in vivo.PLoS biology · 2020Article
- Multiclass classification of autofluorescence images of oral cavity lesions based on quantitative analysis.PloS one · 2020Article
- NEAT1 is overexpressed in Parkinson's disease substantia nigra and confers drug-inducible neuroprotection from oxidative stress.FASEB journal : official publication of the Federation of American Societies for Experimental Biology · 2019Article
- MicroRNA-210-3p Targets RGMA to Enhance the Angiogenic Functions of Endothelial Progenitor Cells Under Hypoxic Conditions.Frontiers in cellular neuroscience · 2019Article
Corrections and comments
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Authors and funding
6 authors at 1 institution in 1 country.
Funding
Abstract
Three-dimensional structures in biological systems are routinely evaluated using large image stacks acquired from fluorescence microscopy; however, analysis of such data is muddled by variability in the signal across and between samples. Here, we present Intensify3D: a user-guided normalization algorithm tailored for overcoming common heterogeneities in large image stacks. We demonstrate the use of Intensify3D for analyzing cholinergic interneurons of adult murine brains in 2-Photon and Light-Sheet fluorescence microscopy, as well as of mammary gland and heart tissues. Beyond enhancement in 3D visualization in all samples tested, in 2-Photon in vivo images, this tool corrected errors in feature extraction of cortical interneurons; and in Light-Sheet microscopy, it enabled identification of individual cortical barrel fields and quantification of somata in cleared adult brains. Furthermore, Intensify3D enhanced the ability to separate signal from noise. Overall, the universal applicability of our method can facilitate detection and quantification of 3D structures and may add value to a wide range of imaging experiments.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.